Whole genome amplification (WGA) can be performed using three types of chemistry: Primer Extension Preamplification PCR (PEP-PCR), degenerate oligonucleotide primer PCR (DOP-PCR), and multiple displacement amplification (MDA). MDA, particularly Phi 29 DNA polymerase based MDA, is the method most frequently employed, and is a less biased amplification method for WGA (Dean et al., Proc Natl Acad Sci USA 99:5261-5266, 2002; Pinard et al., BMC Genomics 7:216-236, 2006; Uda et al., Jpn J Infect Dis. 60:355-361, 2007). However, existing methods using Phi 29 can have a higher allelic dropout rate and less sensitivity for some applications where the amount of genomic DNA in the reaction is limited. Further, it has been suggested that Phi 29 DNA polymerase-based WGA can exhibit unbalanced or uneven amplification across the genome due to the nature of the enzyme (Zong et al., Science 338:1622-1626, 2012; Lage et al., Genome Res. 13: 294-307, 2003). An improved method for single-cell WGA is thus needed to facilitate single-cell genome research.